Complementary Use of NMR to X-Ray Crystallography for the Analysis of Protein Morphological Change in Solution

Abstract

A vast amount of protein structure data is going to pave new ways in protein structure research. They improved the quality of predicted protein structure from its primary sequence (Sanchez and Sali 2000). The possible protein interaction sites to small ligand and/or the other proteins could be predicted based on the protein complex structures in the Protein Data Bank (PDB) (Morris et al. 2009). The combined use of bioinformatics with the protein structure data has been frequently giving invaluable outcomes to facilitate the understanding on the experimental results in biochemistry and molecular biology. In silico protein structure analyses are now already essential approaches in protein research. Protein structural data, most of which came from X-ray crystallography, are also useful to expand the protein structure analysis in solution, when combined with NMR. NMR chemical shift perturbation of a protein caused by the interaction with a compound, for example, allows sensitive identification of the interaction sites on protein (Shuker et al. 1996). This NMR derived binding site information with the protein structure facilitates drug design (Hajduk et al. 1997). This chemical shift-based approach is also applied to the protein-protein interaction, which enables to build a model protein complex structure (de Vries, van Dijk and Bonvin 2010, Dominguez, Boelens and Bonvin 2003). Although these approaches are now prevailingly used, there are limitations in their application. The approaches assume that the target protein retains the X-ray structure in solution and also negates the possible structural change caused by binding to a compound or a partner protein. Some of the proteins are known to have different domain arrangement from those in crystal (Skrynnikov et al. 2000a); it is often the case for the protein having domains linked by flexible linker. In addition, it is commonly found that proteins show structural change in response to compound binding or interaction with the other protein (Evenas et al. 2001). To expand the utility of protein structure data in the PDB in solution protein science, we need new NMR techniques to overcome the known limitations in the existing approaches, which could determine the structure changed from the one by X-ray in binding to a ligand or a partner protein to improve the modelled complex structure, for example. Protein structure change caused by interaction with other molecules is primarily important in discussing protein functional regulation. The structural change is not limited in the region around the binding site. Sometimes, it also causes rather global change including domain